Population genetic structure of the pelagic narrow-barred Spanish mackerel (Scomberomorus commerson) was examined in 10 populations from the Indo-West Pacific region, based on mitochondrial control region DNA. We examined genetic composition of 56 individuals of S. commerson from the Arabian Sea, Bay of Bengal, and compared them with 40 individuals from previously published data sampled from the ROPME Seas area and South West Pacific Ocean. The overall nucleotide and haplotype diversities were estimated to be 0.072 and 0.995, respectively. Demographic parameters such as Tajima’s D and Fu’s F s statistics were negative, but non-significant across all the populations, except for New Caledonia in the South West Pacific, indicating a stable population of S. commerson in this region. To assess intra-specific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated time of most recent population expansion. AMOVA and F ST values among Indian and Arabian regions revealed non-significant variation among the populations, while separation was noted among the samples of the northern and eastern Indian oceans, as well as with South West Pacific. A parsimony network analysis provided evidence for four separate population segment/stocks in the Indian Ocean and Pacific Ocean, raising a conservation concern. Our results support a need for regional cooperation to ensure the sustainable exploitation of S. commerson in the Indo-West Pacific region.